Structural effects of modified ribonucleotides and magnesium in transfer RNAs.

摘要: Modified nucleotides are ubiquitous and important to tRNA structure function. To understand their effect on conformation, we performed a series of molecular dynamics simulations yeast tRNAPhe tRNAinit, Escherichia coli tRNAinit HIV tRNALys. Simulations were with the wild type modified nucleotides, using recently developed CHARMM compatible force field parameter set for (J. Comput. Chem.2016, 37, 896), or corresponding unmodified in presence absence Mg2+. Results showed stabilizing associated modifications Mg2+ some positions, such as guanosine position 37 dihydrouridines 16/17 including both structural properties base interactions. Some other also found make subtle contributions local domains. While not able investigate adenosine limitations observed conformation E. better maintained features interactions systems than indicating utility incorporating RNAs.